Identification of Fur regulated genes in the bacterial fish pathogen Photobacterium damselae ssp. piscicida using the Fur titration assay

The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae

IMPORTANCE

This study highlights diversity in iron acquisition and regulation in bacteria. The mechanisms of iron acquisition and its regulation in Teredinibacter turnerae, as well as its connection to cellulose utilization, a hallmark phenotype of T. turnerae, expand the paradigm of bacterial iron acquisition. Two of the four TonB genes identified in T. turnerae exhibit functional redundancy and play a crucial role in siderophore-mediated iron transport. Unlike typical TonB genes in bacteria, none of the TonB genes in T. turnerae are clearly iron regulated. This unusual regulation could be explained by another important finding in this study, namely, that the two TonB genes involved in iron transport are also essential for cellulose utilization as a carbon source, leading to the expression of TonB genes even under iron-rich conditions.

The Sigma Factor AsbI Is Required for the Expression of Acinetobactin Siderophore Transport Genes in Aeromonas salmonicida

Aeromonas salmonicida subsp. salmonicida (A. salmonicida), a Gram-negative bacterium causing furunculosis in fish, produces the siderophores acinetobactin and amonabactins in order to extract iron from its hosts. While the synthesis and transport of both systems is well understood, the regulation pathways and conditions necessary for the production of each one of these siderophores are not clear. The acinetobactin gene cluster carries a gene (asbI) encoding a putative sigma factor belonging to group 4 σ factors, or, the ExtraCytoplasmic Function (ECF) group. By generating a null asbI mutant, we demonstrate that AsbI is a key regulator that controls acinetobactin acquisition in A. salmonicida, since it directly regulates the expression of the outer membrane transporter gene and other genes necessary for Fe-acinetobactin transport. Furthermore, AsbI regulatory functions are interconnected with other iron-dependent regulators, such as the Fur protein, as well as with other sigma factors in a complex regulatory network.

The dual role of TonB genes in turnerbactin uptake and carbohydrate utilization in the shipworm symbiont Teredinibacter turnerae

Teredinibacter turnerae is an intracellular bacterial symbiont that resides in the gills of shipworms, wood-eating bivalve mollusks. This bacterium produces a catechol siderophore, turnerbactin, required for the survival of this bacterium under iron limiting conditions. The turnerbactin biosynthetic genes are contained in one of the secondary metabolite clusters conserved among T. turnerae strains. However, Fe(III)-turnerbactin uptake mechanisms are largely unknown. Here, we show that the first gene of the cluster, fttA a homologue of Fe(III)-siderophore TonB-dependent outer membrane receptor (TBDR) genes is indispensable for iron uptake via the endogenous siderophore, turnerbactin, as well as by an exogenous siderophore, amphi-enterobactin, ubiquitously produced by marine vibrios. Furthermore, three TonB clusters containing four tonB genes were identified, and two of these genes, tonB1b and tonB2, functioned not only for iron transport but also for carbohydrate utilization when cellulose was a sole carbon source. Gene expression analysis revealed that none of the tonB genes and other genes in those clusters were clearly regulated by iron concentration while turnerbactin biosynthesis and uptake genes were up-regulated under iron limiting conditions, highlighting the importance of tonB genes even in iron rich conditions, possibly for utilization of carbohydrates derived from cellulose.

A proteomic analysis of the iron response of Photobacterium damselae subsp. damselae reveals metabolic adaptations to iron levels changes and novel potential virulence factors

Photobacterium damselae subsp. damselae (Pdd) is a marine bacterium that can infect numerous species of marine fish as well as other species including humans. Low iron availability is one of the signs that bacterial pathogens can detect in order to begin colonizing their host, and the reduction of iron levels is a nonspecific host defense strategy that prevents bacterial proliferation. In this work a proteomic approach was used to study the gene expression adaptations of a Pdd strain in response to iron availability. A comparative analysis of induced proteins in both high- and low-iron conditions showed profound cellular metabolic adaptations that result, for instance, in amino acid requirement. It also provided important information about the changes that occur in the energetic metabolism induced by the surrounding iron levels, allowing for the identification of novel potential virulence factors. Among others, genes involved in the synthesis and transport of a vibrioferrin-like siderophore were identified for the first time. In addition to plasmid pPHDD1-encoded Dly and HlyA hemolysins, a pPHDD1-borne operon, which may encode a transferrin receptor, was also found. This operon identification suggests that this virulence plasmid could encode so-far unknown additional virulence factors other than hemolysins.

Transcriptional regulation by Ferric Uptake Regulator (Fur) in pathogenic bacteria

In the ancient anaerobic environment, ferrous iron (Fe²⁺) was one of the first metal cofactors. Oxygenation of the ancient world challenged bacteria to acquire the insoluble ferric iron (Fe³⁺) and later to defend against reactive oxygen species (ROS) generated by the Fenton chemistry. To acquire Fe³⁺, bacteria produce low-molecular weight compounds, known as siderophores, which have extremely high affinity for Fe³⁺. However, during infection the host restricts iron from pathogens by producing iron- and siderophore-chelating proteins, by exporting iron from intracellular pathogen-containing compartments, and by limiting absorption of dietary iron. Ferric Uptake Regulator (Fur) is a transcription factor which utilizes Fe²⁺ as a corepressor and represses siderophore synthesis in pathogens. Fur, directly or indirectly, controls expression of enzymes that protect against ROS damage. Thus, the challenges of iron homeostasis and defense against ROS are addressed via Fur. Although the role of Fur as a repressor is well-documented, emerging evidence demonstrates that Fur can function as an activator. Fur activation can occur through three distinct mechanisms (1) indirectly via small RNAs, (2) binding at cis regulatory elements that enhance recruitment of the RNA polymerase holoenzyme (RNAP), and (3) functioning as an antirepressor by removing or blocking DNA binding of a repressor of transcription. In addition, Fur homologs control defense against peroxide stress (PerR) and control uptake of other metals such as zinc (Zur) and manganese (Mur) in pathogenic bacteria. Fur family members are important for virulence within bacterial pathogens since mutants of fur, perR, or zur exhibit reduced virulence within numerous animal and plant models of infection. This review focuses on the breadth of Fur regulation in pathogenic bacteria.

Novel iron-regulated and Fur-regulated small regulatory RNAs in Aggregatibacter actinomycetemcomitans

Iron can regulate biofilm formation via non-coding small RNA (sRNA). To determine if iron-regulated sRNAs are involved in biofilm formation by the periodontopathogen Aggregatibacter actinomycetemcomitans, total RNA was isolated from bacteria cultured with iron supplementation or chelation. Transcriptional analysis demonstrated that the expression of four sRNA molecules (JA01-JA04) identified by bioinformatics was significantly upregulated in iron-limited medium compared with iron-rich medium. A DNA fragment encoding each sRNA promoter was able to titrate Escherichia coli ferric uptake regulator (Fur) from a Fur-repressible reporter fusion in an iron uptake regulator titration assay. Cell lysates containing recombinant AaFur shifted the mobility of sRNA-specific DNAs in a gel shift assay. Potential targets of these sRNAs, determined in silico, included genes involved in biofilm formation. The A. actinomycetemcomitans overexpressing JA03 sRNA maintained a rough phenotype on agar, but no longer adhered to uncoated polystyrene or glass, although biofilm determinant gene expression was only modestly decreased. In summary, these sRNAs have the ability to modulate biofilm formation, but their functional target genes remain to be confirmed.

The ABC-transporter hutCD genes of Photobacterium damselae subsp. piscicida are essential for haem utilization as iron source and are expressed during infection in fish

The marine fish pathogen Photobacterium damselae subsp. piscicida utilizes haem compounds as the sole iron source. In a previous work, we characterized a gene cluster with ten potential haem uptake and utilization genes. Two of these genes, hutC and hutD, which are iron-regulated, conform a putative inner membrane haem ABC transporter. In this study, we constructed an insertional mutant, leading to the inactivation of hutCD genes. Reverse transcriptase-PCR analyses demonstrated that an insertion between the hutB and hutC genes abolished transcription of the downstream hutC and hutD genes. The hutCD mutant was unable to utilize haem as the sole iron source, demonstrating that the putative ABC-transporter proteins HutC and HutD are essential for haem utilization as an iron source in P. damselae subsp. piscicida. In addition, reverse transcriptase-PCR assays conducted with RNA samples isolated from experimentally infected fish revealed the presence of hutCD transcripts. The results demonstrate for the first time that haem uptake genes of a fish pathogen are expressed during the infective process in fish.

The iron stimulon of Xylella fastidiosa includes genes for type IV pilus and colicin V-like bacteriocins

Xylella fastidiosa is the etiologic agent of a wide range of plant diseases, including citrus variegated chlorosis (CVC), a major threat to citrus industry. The genomes of several strains of this phytopathogen were completely sequenced, enabling large-scale functional studies. DNA microarrays representing 2,608 (91.6%) coding sequences (CDS) of X. fastidiosa CVC strain 9a5c were used to investigate transcript levels during growth with different iron availabilities. When treated with the iron chelator 2,2'-dipyridyl, 193 CDS were considered up-regulated and 216 were considered down-regulated. Upon incubation with 100 microM ferric pyrophosphate, 218 and 256 CDS were considered up- and down-regulated, respectively. Differential expression for a subset of 44 CDS was further evaluated by reverse transcription-quantitative PCR. Several CDS involved with regulatory functions, pathogenicity, and cell structure were modulated under both conditions assayed, suggesting that major changes in cell architecture and metabolism occur when X. fastidiosa cells are exposed to extreme variations in iron concentration. Interestingly, the modulated CDS include those related to colicin V-like bacteriocin synthesis and secretion and to functions of pili/fimbriae. We also investigated the contribution of the ferric uptake regulator Fur to the iron stimulon of X. fastidiosa. The promoter regions of the strain 9a5c genome were screened for putative Fur boxes, and candidates were analyzed by electrophoretic mobility shift assays. Taken together, our data support the hypothesis that Fur is not solely responsible for the modulation of the iron stimulon of X. fastidiosa, and they present novel evidence for iron regulation of pathogenicity determinants.

A siderophore biosynthesis gene cluster from the fish pathogen Photobacterium damselae subsp. piscicida is structurally and functionally related to the Yersinia high-pathogenicity island

Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, produces a siderophore which is distinct from that produced by P. damselae subsp. damselae. Using suppression subtractive hybridization, a subsp. piscicida-specific DNA region of 35 kb was identified in strain DI21, and 11 genes were defined: dahP, araC1, araC2, frpA, irp8, irp2, irp1, irp3, irp4, irp9 and irp5. The sequence of the predicted proteins encoded by these genes showed significant similarity with the proteins responsible for the synthesis and transport of the siderophore yersiniabactin, encoded within the Yersinia high-pathogenicity island (HPI). Southern hybridization demonstrated that this gene cluster is exclusive to some European subsp. piscicida isolates. Database searches revealed that a similar gene cluster is present in Photobacterium profundum SS9 and Vibrio cholerae RC385. An irp1 gene (encoding a putative non-ribosomal peptide synthetase) insertional mutant (CS31) was impaired for growth under iron-limiting conditions and unable to produce siderophores, and showed an approximately 100-fold decrease in degree of virulence for fish. The subsp. piscicida DI21 strain, but not CS31, promoted the growth of a Yersinia enterocolitica irp1 mutant. Furthermore, a yersiniabactin-producing Y. enterocolitica strain as well as purified yersiniabactin were able to cross-feed strains DI21 and CS31, suggesting that the subsp. piscicida siderophore might be functionally and structurally related to yersiniabactin. The differential occurrence among P. damselae strains, and the low sequence similarity to siderophore synthesis genes described in other members of the Vibrionaceae, suggest that this genetic system might have been acquired by horizontal transfer in P. damselae subsp. piscicida, and might have a common evolutionary origin with the Yersinia HPI.

Heme, an iron supply for vibrios pathogenic for fish

One of the main mechanisms present in gram-negative bacterial pathogens to obtain iron is the utilization of free heme or heme proteins from the host tissues. Vibrio anguillarum, the etiological agent of vibriosis in fish, and Photobacterium damselae subsp. piscicida, the causative agent of fish pasteurellosis, can acquire iron from free heme or heme-containing proteins present in the host tissues by a siderophore-independent mechanism. Similarly to other animal and human pathogens, the general mechanism for heme uptake in these two species consists in the presence of an outer membrane receptor that transport the heme molecule into the periplasm via a TonB-dependent process, and additional proteins that complete the transport of heme from the periplasm into the cell cytoplasm. Expression of heme uptake genes is iron-regulated at the transcriptional level by the repressor protein Fur. The heme uptake mechanisms are believed to contribute to virulence for fish. The existence of variability in the distribution of heme transport genes among strains suggests that gene inactivation and/or horizontal transfer might play a significant role in generating intraspecific genetic diversity.

Subtractive hybridization reveals a high genetic diversity in the fish pathogen Photobacterium damselae subsp. piscicida: evidence of a SXT-like element

Photobacterium damselae subsp. piscicida is the causative agent of fish pasteurellosis, a severe disease affecting cultured marine fish worldwide. In this study, suppression subtractive hybridization was used to identify DNA fragments present in the virulent strain PC554.2, but absent in the avirulent strain EPOY 8803-II. Twenty-one genomic regions of this type (that included twenty-six distinct putative ORFs) were analysed by DNA sequencing. Twenty ORFs encoded proteins with homology to proteins in other bacteria, including four homologues involved in siderophore biosynthesis, and four homologues related to mobile elements; three of these were putative transposases and one was a putative conjugative transposon related to the Vibrio cholerae SXT element. This sequence was shown to be integrated into a prfC gene homologue. Six ORFs showed no significant homology to known bacterial proteins. Among the 21 DNA fragments specific to strain PC554.2, 5 DNA fragments (representing 7 ORFs) were also absent in the avirulent strain ATCC 29690. The analysis of these differential regions, as well as the screening of their presence in a collection of strains, demonstrated the high genetic heterogeneity of this pathogen.

Heme uptake genes in human and fish isolates of Photobacterium damselae: existence of hutA pseudogenes

The marine bacterium Photobacterium damselae includes strains classified into two distinct subspecies, namely subsp. damselae and subsp. piscicida, which have been reported to cause disease in a variety of marine animals and in humans. P. damselae strains utilize heme compounds as sole iron sources. In the present study, ten potential heme uptake and utilization genes are described in P. damselae subsp. damselae and subsp. piscicida. One gene cluster includes the genes coding for putative proteins HutZ, HutX and HutW; TonB, ExbB and ExbD, the three components of the TonB system; HutB, the putative periplasmic binding protein; HutC, the putative inner membrane permease; and HutD, the putative ABC-transporter ATP-ase. A gene coding for HutA, the outer membrane heme receptor, has also been identified, but it is not linked to the rest of the heme transport genes. RT-PCR analyses showed that heme uptake genes are arranged in three iron-regulated transcriptional units. A plasmid carrying the gene for the heme receptor HutA in combination with a plasmid carrying tonBexbBDhutBCD genes conferred to Escherichia coli 101ESD (ent) the ability to use heme and hemoglobin as iron sources. The hutA gene was present in strains isolated from humans and a variety of fish species, but it was shown to be interrupted in some subsp. piscicida strains, constituting a pseudogene. This is the first description of a heme-uptake system in a Photobacterium species, and shows some structural and functional similarities to heme-uptake systems reported in other gram-negative bacteria.